Abstract—Long Terminal Repeat transposable elements (LTRs) are a major type of mobile elements ubiquitous in eukaryotic genomes. They account for a major proportion of many plant genomes and have a prominent impact on the evolution of genome size, structure and function. Although some bioinformatics tools for de novo LTR identification from genome sequences have been developed, an automated and standardized software tool for both LTR identification and annotation would be valuable and essential for comparative analysis of sequenced plant genomes. We present here a Java-based pipeline tool, called LTR Annotator, for automatically and consistently performing genome-wide de novo identification and annotation of LTRs of plant genome sequences. The pipeline first identifies LTRs using both LTR_FINDER and LTR harvest, then performs intensive annotations, and finally sweeps out potentially false-positive LTRs. The pipeline was evaluated using the well curated Arabidopsis genome. High sensitivity (>0.9) was obtained using LTR harvest or LTR harvest+LTR_FINDER. Ten potentially new intact LTRs were detected. This pipeline provides a comprehensive tool to perform comparative analysis of LTRs for plant genomes, delivering annotated genomic resources for epigenetic and other studies. LTR Annotator is free and available upon request.